Emerald is one tough bastard, although slightly weaker than his bigger, badder, brother, Ruby. He has 1,000,000 HP, and has devastating physical attacks. He also has an attack called Aire Tam Storm, which deals damage based on how much materia your party has equipped, so you cannot rely on tons of materia to win the day. Of course, if you have final attack materia paired with Phoenix, you can circumvent this. Unlike Ruby, Emerald will not counter-attack KOTR with Ultima, and so for this reason is much easier. In order to get rid of the 20 minute timer, however, you will need to use the morph ability on a Ghost Ship enemy (you can find them in the Underwater Reactor, just before the reactor itself so they're not missable) and obtain an Underwater Map item. Head to Kalm and talk to the Kalm Traveller, and he will give you the Underwater materia. If you speak to him after defeating Emerald, he will give you a set of Master Materia in exchange for the Earth Harp Emerald drops.